JSDM models test
Data description
Data was simulated using VirtualCommunity code.
Simulated data contains 20 data sets.
In this file we have compared the 3 models HMSC,GJAM, JSDM on 21 simulated Dataset.\ We have compared the ability to recover the true interactions used for modelling this datasets, by comparing estimated correlation matrix and matrix representing true interactions.
There is a separate file, with the functions needed to fit each model and study the convergence and more parameters are presented.
## Environment filtering 5 species
JSDM
GJAM
HMSC
Convergence:
Study of interactions
Plot species responses
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
Plot coefficients
ALL3<-function(jsdm_mod,gjam_mod,hmsc_mod,interact=diag(5)){
par(mfrow=c(2,2),oma = c(1, 1, 1, 1))
corrplot(jsdm_mod, diag = FALSE, order = "original",tl.pos = "ld", tl.cex = 0.5, method = "color",col=cols(200), type = "lower")
title("R JSDM ")
corrplot(gjam_mod, diag = FALSE, order = "original",tl.pos = "ld", tl.cex = 0.5, method = "color",col=cols(200), type = "lower")
title("R GJAM")
corrplot(hmsc_mod, diag = FALSE, order = "original",tl.pos = "ld", tl.cex = 0.5, method = "color",col=cols(200), type = "lower")
title("R HMSC")
corrplot(interact, diag = FALSE, order = "original",tl.pos = "ld", tl.cex = 0.5, method = "color",col=cols(200), type = "lower")
title("True interactions")
}
ALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc,diag(5))
ALL4<-function(jsdm_mod,gjam_mod,hmsc_mod,interact=diag(5)){
par(mfrow=c(2,2),oma = c(1, 1, 1, 1))
#corrplot(jsdm_mod, diag = FALSE, order = "original",tl.pos = "ld", tl.cex = 0.5, method = "color",col=cols(200), type = "lower")
#title("Partial correlation JSDM ")
corrplot(gjam_mod, diag = FALSE, order = "original",tl.pos = "ld", tl.cex = 0.5, method = "color",col=cols(200), type = "lower")
title("Partial correlation GJAM")
corrplot(hmsc_mod, diag = FALSE, order = "original",tl.pos = "ld", tl.cex = 0.5, method = "color",col=cols(200), type = "lower")
title("Partial correlation HMSC")
corrplot(interact, diag = FALSE, order = "original",tl.pos = "ld", tl.cex = 0.5, method = "color",col=cols(200), type = "lower")
title("True interactions")
}
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc,diag(5))
Environmental filtering 10 species
JSDM
Gjam
HMSC
create_beta_plot(load_object("./gjam_models/gjam10env.rda"),me10,load_object("./HMmodels/hm10env.rda"))
create_plot_response(data=sim_data$EnvEvenSp10, nsp=10,pred_gjam, pred_jsdm,pred_hmsc )
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per pageALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc,diag(10))
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc,diag(10))
Environmental filtering 20 species
JSDM
Gjam
Gjam dimension reduction
create_beta_plot(load_object("./gjam_models/gjam20env.rda"),me10,load_object("./HMmodels/hm20env.rda"))
create_plot_response(sim_data$EnvEvenSp20, nsp=5,pred_gjam, pred_jsdm,pred_hmsc )
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per pageALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc,diag(20))
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc,diag(20))
Environmental filtering + Facilitation dense 5 species
JSDM
Gjam
HMSC
create_beta_plot(load_object("./gjam_models/gjam20env.rda"),me10,load_object("./HMmodels/hm20env.rda"))
create_plot_response(sim_data$EnvEvenSp20, nsp=5,pred_gjam, pred_jsdm,pred_hmsc )
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per pageALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc,fac_inter[[4]])
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc,diag(10))
Environmental filtering + Facilitation dense 10 species
JSDM
HMSC
create_beta_plot(load_object("./gjam_models/gjam20env.rda"),me10,load_object("./HMmodels/hm20env.rda"))
create_plot_response(sim_data$EnvEvenSp20, nsp=5,pred_gjam, pred_jsdm,pred_hmsc )
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per pageALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc,fac_inter[[5]])
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc,fac_inter[[5]])
Environmental filtering + Facilitation dense 20 species
JSDM
Gjam
HMSC
create_beta_plot(load_object("./gjam_models/gjam20env.rda"),me10,load_object("./HMmodels/hm20env.rda"))
create_plot_response(sim_data$EnvEvenSp20, nsp=5,pred_gjam, pred_jsdm,pred_hmsc )
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per pageALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc,fac_inter[[6]])
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc,fac_inter[[6]])
Environmental filtering + Facilitation sparse 5 species
JSDM
Gjam
HMSC
create_beta_plot(load_object("./gjam_models/gjam20env.rda"),me10,load_object("./HMmodels/hm20env.rda"))
create_plot_response(sim_data$EnvEvenSp20, nsp=5,pred_gjam, pred_jsdm,pred_hmsc )
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per pageALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc,fac_inter[[7]])
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc,fac_inter[[7]])
Environmental filtering + Facilitation sparse 10 species
JSDM
HMSC
create_beta_plot(load_object("./gjam_models/gjam20env.rda"),me10,load_object("./HMmodels/hm20env.rda"))
create_plot_response(sim_data$EnvEvenSp20, nsp=5,pred_gjam, pred_jsdm,pred_hmsc )
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per pageALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc,fac_inter[[8]])
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc,fac_inter[[8]])
Environmental filtering + Facilitation sparse 20 species
JSDM
Gjam
HMSC
HMSC
create_beta_plot(load_object("./gjam_models/gjam20env.rda"),me10,load_object("./HMmodels/hm20env.rda"))
create_plot_response(sim_data$EnvEvenSp20, nsp=5,pred_gjam, pred_jsdm,pred_hmsc )
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per pageALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc,fac_inter[[9]])
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc,fac_inter[[9]])
Environmental filtering + Competition dense 5 species
JSDM
Gjam
create_beta_plot(load_object("./gjam_models/gjam20env.rda"),me10,load_object("./HMmodels/hm20env.rda"))
create_plot_response(sim_data$EnvEvenSp20, nsp=5,pred_gjam, pred_jsdm,pred_hmsc )
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per pageALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc,(-1)*comp_inter[[10]])
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc,(-1)*comp_inter[[10]])
Environmental filtering + Competition dense 10 species
Gjam
HMSC
create_beta_plot(load_object("./gjam_models/gjam20env.rda"),me10,load_object("./HMmodels/hm20env.rda"))
create_plot_response(sim_data$EnvEvenSp20, nsp=5,pred_gjam, pred_jsdm,pred_hmsc )
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per pageALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc,(-1)*comp_inter[[11]])
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc,(-1)*comp_inter[[11]])
Environmental filtering + Competition dense 20 species
Gjam
HMSC
create_beta_plot(load_object("./gjam_models/gjam20env.rda"),me10,load_object("./HMmodels/hm20env.rda"))
create_plot_response(sim_data$EnvEvenSp20, nsp=5,pred_gjam, pred_jsdm,pred_hmsc )
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per pageALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc,(-1)*comp_inter[[12]])
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc,(-1)*comp_inter[[12]])
Environmental filtering + Competition sparse 5 species
Gjam
HMSC
create_beta_plot(load_object("./gjam_models/gjam5cmps.rda"),cmps5,load_object("./HMmodels/hm5cmps.rda"))
create_plot_response(sim_data$CompSparseSp5, nsp=5,pred_gjam, pred_jsdm,pred_hmsc )
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per pageALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc,(-1)*comp_inter[[13]])
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc,(-1)*comp_inter[[13]])
Environmental filtering + Competition sparse 10 species
JSDM
Gjam
create_beta_plot(load_object("./gjam_models/gjam10cmps.rda"),cmps10,load_object("./HMmodels/hm10cmps.rda"))
create_plot_response(sim_data$CompSparseSp10, nsp=10,pred_gjam, pred_jsdm,pred_hmsc )
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per pageALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc,(-1)*comp_inter[[14]])
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc,(-1)*comp_inter[[14]])
Environmental filtering + Competition sparse 20 species
JSDM
Gjam
HMSC
create_beta_plot(load_object("./gjam_models/gjam20cmps.rda"),cmps20,load_object("./HMmodels/hm20cmps.rda"))
create_plot_response(sim_data$CompSparseSp20, nsp=20,pred_gjam, pred_jsdm,pred_hmsc )
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per pageALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc,(-1)*comp_inter[[15]])
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc,(-1)*comp_inter[[15]])
Environmental filtering + Competition +Facilitation 5 dense species
JSDM
Gjam
HMSC
create_beta_plot(load_object("./gjam_models/gjam5cmp_facd2.rda"),cmp_fd5,load_object("./HMmodels/hmcmp_facd5.rda"))
create_plot_response(sim_data$FacCompDenseSp5, nsp=5,pred_gjam, pred_jsdm,pred_hmsc )
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per pageALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc, (-1)*comp_inter[[16]]+ fac_inter[[16]])
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc, (-1)*comp_inter[[16]]+ fac_inter[[16]])
Environmental filtering + Competition +Facilitation 10 dense species
JSDM
Gjam
HMSC
create_beta_plot(load_object("./gjam_models/gjamcmp_facd10.rda"),cmp_fd10,load_object("./HMmodels/hmcmp_facd10.rda"))
create_plot_response(sim_data$FacCompDenseSp10, nsp=10,pred_gjam, pred_jsdm,pred_hmsc )
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per pageALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc, (-1)*comp_inter[[17]]+ fac_inter[[17]])
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc, (-1)*comp_inter[[17]]+ fac_inter[[17]])
Environmental filtering + Competition +Facilitation 20 dense species
JSDM
Gjam
HMSC
create_beta_plot(load_object("./gjam_models/gjamcmp_facd20.rda"),cmp_fd20,load_object("./HMmodels/hmcmp_facd20.rda"))
create_plot_response(sim_data$FacCompDenseSp20, nsp=20,pred_gjam, pred_jsdm,pred_hmsc )
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per pageALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc, (-1)*comp_inter[[18]]+ fac_inter[[18]])
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc, (-1)*comp_inter[[18]]+ fac_inter[[18]])
Environmental filtering + Competition +Facilitation 5 sparse species
JSDM
Gjam
HMSC
create_beta_plot(load_object("./gjam_models/gjamcmp_facs5.rda"),cmp_fds5,load_object("./HMmodels/hmcmp_facs5.rda" ))
create_plot_response(sim_data$FacCompSparseSp5, nsp=5,pred_gjam, pred_jsdm,pred_hmsc )
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per pageALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc, (-1)*comp_inter[[19]]+ fac_inter[[19]])
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc, (-1)*comp_inter[[19]]+ fac_inter[[19]])
Environmental filtering + Competition +Facilitation 10 sparse species
JSDM
Gjam
HMSC
create_beta_plot(load_object("./gjam_models/gjamcmp_facs10.rda"),cmp_fds10,load_object("./HMmodels/hmcmp_facs10.rda"))
create_plot_response(sim_data$FacCompSparseSp10, nsp=10,pred_gjam, pred_jsdm,pred_hmsc )
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per pageALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc, (-1)*comp_inter[[20]]+ fac_inter[[20]])
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc, (-1)*comp_inter[[20]]+ fac_inter[[20]])
Environmental filtering + Competition +Facilitation 20 sparse species
JSDM
Gjam
HMSC
create_beta_plot(load_object("./gjam_models/gjamcmp_facs20.rda"),cmp_fds20,load_object("./HMmodels/hmcmp_facs20.rda"))
create_plot_response(sim_data$FacCompSparseSp20, nsp=20,pred_gjam, pred_jsdm,pred_hmsc )
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per page
## Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-
## transparency is not supported on this device: reported only once per pageALL3(mod_list_Rho$jsdm,mod_list_Rho$gjam,mod_list_Rho$hmsc, (-1)*comp_inter[[21]]+ fac_inter[[21]])
ALL4(mod_list_Tau$jsdm,mod_list_Tau$gjam,mod_list_Tau$hmsc, (-1)*comp_inter[[21]]+ fac_inter[[21]])
Graph from paper
Visualization for true interactions
Facilitation
Competition Dense
Competition Dense
Competition + Facilitation Dense
Competition + Facilitation Sparse
